Having been lost in space for years aboard the Forward Unto Dawn, Cortana wakes Master Chief shortly before Covenant forces board the vessel as it approaches Requiem. The remnants of the Dawn are caught in Requiem's gravity well and pass through an opening on the planet's surface to crash on Requiem's interior.
Cortana confirms that the Covenant forces opposing the Chief are a splinter faction called the "Storm"; they are also opposed by cybernetic constructs called Prometheans. She reveals that the normal lifespan of an AI is seven years and she is currently in her eighth year. Her exposure to Halo and her operation beyond her natural lifespan have contributed to her becoming "rampant", a mental state of aged AIs akin to insanity, and which normally results in the "death" of the AI. She also receives radio signals from a human ship, the UNSC Infinity, whose captain, Andrew Del Rio, and executive officer, Thomas Lasky, have picked up the distress beacon from the Dawn. Cortana tries to warn them away, lest they also be dragged into the gravity well, and directs the Chief to the source of a jamming signal that is interfering with her broadcasts. Unfortunately, it is actually a trap laid by the Didact, a Forerunner first introduced in Halo Legends, who has summoned both the Storm Covenant and now John-117. John inadvertently frees the Didact from his imprisonment, and the Didact, now supported by both Storm Covenant and Prometheans, sets out to achieve his goals, which begins with an assault on the Infinity.
After helping Lasky, Del Rio and Sarah Palmer, member of the SPARTAN-IV corps, repulse the attack on the Infinity, the Master Chief sets out on a mission to destroy the gravity well so that the UNSC ship can escape. Cortana's Rampancy continues to plague her, as she loses her temper and is not always able to complete mission tasks. Additionally, the Chief is contacted by the Librarian, long-deceased Forerunner, protector of humanity, and former wife of the Didact. She explains that after humanity was cast down after their defeat in the Human-Forerunner War (first detailed in Halo: Cryptum), The Flood began to encroach upon the galaxy, and the Forerunners were divided on how to protect humanity from them. The Didact advocated using a device called the "Composer" to convert humans into digital AIs to power up his loyal Prometheans, some of whom the Chief has already fought, and currently seeks this tool as the means to his conquest. The Librarian grants John-117 immunity to the compositing process and returns him to the UNSC forces. The gravity well is successfully demolished, but Captain Del Rio orders a full retreat to Earth instead of staying to oppose the Didact, using Cortana's Rampancy to attack the veracity of her and John's testimony. The Master Chief refuses these orders and remains on Requiem with Cortana.
The Master Chief and Cortana attempt to sabotage the Didact's ship. They are unsuccessful, but by stowing aboard a phantom they are taken to the location of the Composer: the Ivanoff Research Station recently established near Installation 03, one of the remaining Halo rings. Despite the combined efforts of the Chief and Ivanoff research staff to destroy the Composer, the Didact is able to gain custody of it with a gravity beam. He then tests the weapon by firing it at the station, burning the entire crew except for John and Cortana into ash. The Didact then departs for Earth, with John and Cortana pursuing in a Broadsword fighter stowed in the outer hull of the Didact's ship. Aided by a UNSC defense fleet headed by the Infinity, the Chief boards the ship with a nuclear warhead in tow, whilst Cortana takes advantage of her Rampancy-caused personality fragmentation to overwhelm the enemy computer systems. The two together defeat the Didact, and John detonates the bomb. John finds himself in a mysterious region, then Cortana appears. She explains that she used the rest of her power to form a shield of hard light around John's body where she can actually touch him for the first and final time, and is seemingly at peace. John protests this, insisting that he could save her again as they go together, but she welcomes him home and dies when the ship is destroyed. John is later found by a UNSC rescue team and is taken back to the Infinity, where he is left to mourn the loss of Cortana.
In the post-credits video, John returns to Earth for debriefing. The video is overlaid by narration from the Didact, proclaiming the Forerunners as custodians of the galaxy and humanity is their greatest threat. "Think of my acts as you will, but do not doubt the reality: the reclamation has already begun, and we are hopeless to stop it". In the final moments of the scene, John 117 has his armour and helmet removed. If the player completes the game on Legendary difficulty, his eyes are briefly seen when the helmet is removed.